If someone mentions (@) you in a Chat Room, the Rooms icon in Jabber will continue to show the number of unread Mentions until you change the view to "Filters" and open the "My Mentions". That stays open in the Chats list until Jabber is restarted. Then it is gone again.
In Jabber Mobile, at the top of the Rooms list, is a "New Mentions" bar that lets you quickly get to your mentions.
It would be helpful to have the same feature in the Desktop Client.